Molecular identification and studies on genetic diversity and structure-related GC heterogeneity of Spatholobus Suberectus based on ITS2

Liu, X. Y. et al. Anti-inflammatory activity of some characteristic constituents from the vine stems of Spatholobus Suberectus. Molecules. 24 (20), 3750 (2019).Article 
PubMed 
PubMed Central 

Google Scholar 
Li, W. et al. Chemical characterization of procyanidins from Spatholobus Suberectus and their antioxidative and anticancer activities. J. Funct. Foods. 12, 468–477 (2015).Article 

Google Scholar 
Kwon, K. R. et al. Attenuation of UVB-induced photo-aging by polyphenolic-rich Spatholobus suberectus stem extract via modulation of MAPK/AP-1/MMPs signaling in human keratinocytes. Nutrients. 11 (6), 1341 (2019).Article 
PubMed 
PubMed Central 

Google Scholar 
Zhao, P. et al. Spatholobus suberectus exhibits antidiabetic activity in vitro and in vivo through activation of AKT-AMPK pathway. Evid. Based Complement. Alternat Med. 18, 6091923 (2017).Article 

Google Scholar 
Zhang, F. et al. A review of the pharmacological potential of Spatholobus Suberectus Dunn on cancer. Cells. 11 (18), 2885 (2022).Article 
PubMed 
PubMed Central 

Google Scholar 
Qin, S. S. et al. Comparative genomics of Spatholobus suberectus and insight into flavonoid biosynthesis. Front. Plant. Sci. 4 (11), 528108 (2020).Article 

Google Scholar 
Cheng, Y. Y. et al. Analysis of Sheng-Mai-San, a ginseng-containing multiple components traditional Chinese herbal medicine using liquid chromatography tandem mass spectrometry and physical examination by electron and light microscopies. Molecules. 21 (9), 1159 (2016).Article 
PubMed 
PubMed Central 

Google Scholar 
Sun, J. X. et al. Precise identification of Celosia argentea seed and its five adulterants by multiple morphological and chemical means. J. Pharm. Biomed. Anal. 216 (15), 114802 (2022).Article 
PubMed 

Google Scholar 
Li, X. X. et al. Comprehensive identification of Vitex trifolia fruit and its five adulterants by comparison of micromorphological, microscopic characteristics, and chemical profiles. Microsc Res. Tech. 83 (12), 1530–1543 (2022).Article 

Google Scholar 
Chen, S. L. et al. Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS One 5(1), e8613 (2010).Sokołowska, J. et al. Assessment of ITS2 region relevance for taxa discrimination and phylogenetic inference among Pinaceae. Plants. 11 (8), 1078 (2022).Article 
PubMed 
PubMed Central 

Google Scholar 
Gao, Z. T. et al. DNA mini-barcoding: a derived barcoding method for herbal molecular identification. Front. Plant. Sci. 10, 987 (2019).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Coissac, E. et al. From barcodes to genomes: extending the concept of DNA barcoding. Mol. Ecol. 25 (7), 1423–1428 (2016).Article 
PubMed 

Google Scholar 
Hollingsworth, P. M. et al. Telling plant species apart with DNA: from barcodes to genomes. Philos. Trans. R Soc. Lond. B Biol. Sci. 371 (1702), 20150338 (2016).Article 
PubMed 
PubMed Central 

Google Scholar 
China, Plant, B. O. L. et al. Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants. PNAS. 108, 19641–19646 (2011).Article 
ADS 

Google Scholar 
Plant, C. B. O. L. Working. Group. A DNA barcode for land plants. PNAS. 108 (49), 19641–19646 (2011).ADS 

Google Scholar 
Chen, S. L. et al. A renaissance in herbal medicine identification: from morphology to DNA. Biotechnol. Adv. 32 (7), 1237–1244 (2014).Article 
PubMed 

Google Scholar 
Zhang, Z. X. et al. Morphological and physiological responses of Spatholobus Suberectus Dunn to nitrogen and water availability. Photosynthetica. 57 (4), 1130–1141 (2019).Article 

Google Scholar 
Xiao, J. P. et al. Pharmacodynamic material basis and potential mechanism study of Spatholobi Caulis in reversing osteoporosis. Evid-Based Compl Alt. 14, 3071147 (2023).Article 

Google Scholar 
An, R. et al. Molecular identification of Spatholobus Suberectus and its adulterants based on 26S rDNA D1-D3 region sequence analysis. J. Guangzhou Univ. Chin. Med. 27 (04), 403–406 (2010).
Google Scholar 
Huang, Q. L. et al. Analysis and molecular identification of matK gene in Spatholobus Suberectus and its adulterated products. North. Hortic. 17, 94–98 (2015).
Google Scholar 
Zhou, H. et al. Psba-trnh barcode molecular identification of Spatholobi Caulis, Kadsurae Caulis, Sargentodoxa cuneata and other Spatholobi medicinal materials. Modernization Traditional Chin. Med. Materia Medica-World Sci. Technol. 18 (01), 40–45 (2016).
Google Scholar 
Nafisi, H. et al. Characterizing nrDNA ITS1, 5.8S and ITS2 secondary structures and their phylogenetic utility in the legume tribe Hedysareae with special reference to Hedysarum. PLoS One 18(04), e0283847 (2023).Keller, A. et al. 5.8S-28S rRNA interaction and HMM-based ITS2 annotation. Gene. 430 (1–2), 50–57 (2009).Article 
PubMed 

Google Scholar 
Giudicelli, G. C. et al. Secondary structure of nrDNA Internal Transcribed spacers as a useful tool to align highly divergent species in phylogenetic studies. Genet. Mol. Biol. 40 (1 Suppl 1), 191–199 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
Chao, Z. et al. DNA Barcoding Chin. Med. Bupleurum Phytomedicine 21(13), 1767–1773 (2014).
Google Scholar 
Wei, S. et al. Molecular identification and targeted quantitative analysis of medicinal materials from Uncaria species by DNA barcoding and LC-MS/MS. Molecules. 24 (01), 175 (2019).Article 
PubMed 
PubMed Central 

Google Scholar 
Dechbumroong, P. et al. DNA barcoding of Aristolochia plants and development of species-specific multiplex PCR to aid HPTLC in ascertainment of Aristolochia herbal materials. PLoS One 13(8), e0202625 (2018).Acharya, G. C. et al. Molecular phylogeny, DNA barcoding, and ITS2 secondary structure predictions in the medicinally important Eryngium genotypes of east coast region of India. Genes (Basel). 13 (9), 1678 (2022).Article 
PubMed 

Google Scholar 
Zheng, M. et al. Molecular authentication of medicinal and edible plant Gnaphalium affine (cudweed herb, Shu-qu-cao) based on DNA barcode marker ITS2. Acta Physiol. Plant. 43 (8), 119 (2021).Article 

Google Scholar 
Zhou, Y. et al. ITS2 barcode for identifying the officinal rhubarb source plants from its adulterants. Biochem. Syst. Ecol. 70, 177–185 (2017).Article 

Google Scholar 
Khazal, R. M. et al. Genetic diversity of Leishmania major isolated from different dermal lesions using ITS2 region. Acta Parasitol. 69, 831–838 (2024).Article 
PubMed 

Google Scholar 
Delva, E. et al. Genetic diversity of Amylomyces rouxii from Ragi Tapai in Java island based on ribosomal regions ITS1/ITS2 and D1/D2. Mycobiology. 50 (2), 132–141 (2022).Article 
PubMed 
PubMed Central 

Google Scholar 
Lin, Y. et al. Marine conditions in Andaman Sea shape the unique genetic structure of Sargassum Plagiophyllum C. Agardh. J. Appl. Phycol. 36 (1), 501–511 (2024).Article 

Google Scholar 
Mai, J. C. et al. The internal transcribed spacer 2 exhibits a common secondary structure in green algae and flowering plants. J. Mol. Evol. 44 (3), 258–271 (1997).Article 
ADS 
PubMed 

Google Scholar 
Coleman, A. W. ITS2 is a double-edged tool for eukaryote evolutionary comparisons. Trends Genet. 19 (7), 370–375 (2003).Article 
PubMed 

Google Scholar 
Umdale, S. D. et al. Genetic diversity of Asian Vigna species (Subgenus Ceratotropis; Genus Vigna) in India based on ITS2 sequences data. Plant. Mol. Biol. Rep. 41 (3), 454–469 (2023).Article 

Google Scholar 
Li, X. Q. et al. Variation, evolution, and correlation analysis of C + G content and genome or chromosome size in different kingdoms and phyla. PLoS One 9(2), e88339 (2014).Kakimoto, Y. et al. MicroRNA stability in FFPE tissue samples: dependence on GC content. PLoS One 11(9), e0163125 (2016).Chen, H. et al. Analysis of DNA interactions and GC content with energy decomposition in large-scale quantum mechanical calculations. Phys. Chem. Chem. Phys. 23 (14), 8891–8899 (2021).Article 
PubMed 

Google Scholar 
Zhang, J. et al. GC content around splice sites affects splicing through pre-mRNA secondary structures. BMC Genom. 12 (1), 90 (2011).Article 

Google Scholar 
Karro, J. E. et al. Exponential decay of GC content detected by strand-symmetric substitution rates influences the evolution of isochore structure. Mol. Biol. Evol. 25 (2), 362–374 (2007).Article 
PubMed 

Google Scholar 
Liu, Y. et al. GC heterogeneity reveals sequence-structures evolution of angiosperm ITS2. BMC Plant. Biol. 23 (1), 608 (2023).Article 
PubMed 
PubMed Central 

Google Scholar 
Bengtsson-Palme, J. et al. Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods Ecol. Evol. 4, 914–919 (2013).Article 

Google Scholar 
González-Pech, R. A. et al. Commonly misunderstood parameters of NCBI BLAST and important considerations for users. Bioinformatics. 35 (15), 2697–2698 (2018).Article 

Google Scholar 
Nakamura, T. et al. Parallelization of MAFFT for large-scale multiple sequence alignments. Bioinformatics. 34 (14), 2490–2492 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Capella-Gutiérrez, S. et al. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 25 (15), 1972–1973 (2009).Article 
PubMed 
PubMed Central 

Google Scholar 
Darriba, D. et al. ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models. Mol. Biol. Evol. 37 (1), 291–294 (2019).Article 
PubMed Central 

Google Scholar 
Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 30 (9), 1312–1313 (2014).Article 
PubMed 
PubMed Central 

Google Scholar 
Tamura, K. et al. Prospects for inferring very large phylogenies by using the neighbor-joining method. PNAS. 101 (30), 11030–11035 (2004).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Yu, G. et al. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Mol. Biol. Evol. 35 (12), 3041–3043 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Wright, E. & Using DECIPHER v2.0 to analyze big biological sequence data in R. R J. 8 (1), 352–359 (2016).Article 

Google Scholar 
Valero-Mora, P. M. et al. ggplot2: elegant graphics for data analysis. Meas-Interdiscip Res. 17 (3), 160–167 (2019). 2nd ed.
Google Scholar 
Rozas, J. et al. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol. Biol. Evol. 34 (12), 3299–3302 (2017).Article 
PubMed 

Google Scholar 
Paradis, E. Pegas: an R package for population genetics with an integrated–modular approach. Bioinformatics. 26 (3), 419–420 (2010).Article 
PubMed 

Google Scholar 
Benman, R. B. Using RNAFOLD to predict the activity of small catalytic RNAs. Biotechniques. 15 (6), 1090–1095 (1993).
Google Scholar 
Wright, P. R. et al. CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains. Nucleic Acids Res. 42, W119–123 (2014).Article 
PubMed 
PubMed Central 

Google Scholar 
Xian, Q. et al. Structure-based GC investigation sheds new light on ITS2 evolution in Corydalis species. Int. J. Mol. Sci. 24 (9), 7716 (2023).Article 
PubMed 
PubMed Central 

Google Scholar 
Allen, J. E. et al. Assessing the state of substitution models describing noncoding RNA evolution. Genome Biol. Evol. 6 (1), 65–75 (2014).Article 
PubMed 
PubMed Central 

Google Scholar 
Sueoka, N. On the genetic basis of variation and heterogeneity of DNA base composition. PNS. 48 (4), 582–592 (1962).Article 

Google Scholar 
Álvarez, I. et al. Ribosomal ITS sequences and plant phylogenetic inference. Mol. Phylogenet Evol. 29 (3), 417–434 (2003).Article 
PubMed 

Google Scholar 
Lv, Y. N. et al. Identification of medicinal plants within the Apocynaceae family using ITS2 and psba-trnh barcodes. Chin. J. Nat. Med. 18 (8), 594–605 (2020).PubMed 

Google Scholar 
Gao, T. et al. Identification of medicinal plants in the family Fabaceae using a potential DNA barcode ITS2. J. Ethnopharmacol. 130 (1), 116–121 (2010).Article 
PubMed 

Google Scholar 
Feng, S. G. et al. Application of the ribosomal DNA ITS2 region of Physalis (Solanaceae): DNA barcoding and phylogenetic study. Front. Plant. Sci. 7, 1047 (2016).Article 
PubMed 
PubMed Central 

Google Scholar 
Yu, J. et al. Progress in the use of DNA barcodes in the identification and classification of medicinal plants. Ecotox Environ. Safe. 208, 111691 (2021).Article 

Google Scholar 
Kress, W. J. et al. Use of DNA barcodes to identify flowering plants. PNAS. 102 (23), 8369–8374 (2005).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Cahyaningsih, R. et al. DNA barcoding medicinal plant species from Indonesia. Plants. 11 (10), 1375 (2022).Article 
PubMed 
PubMed Central 

Google Scholar 
Meier, R. et al. The use of mean instead of smallest interspecific distances exaggerates the size of the barcoding gap and leads to misidentification. Syst. Biol. 57 (5), 809–813 (2008).Article 
PubMed 

Google Scholar 
Lynch, M. et al. The evolutionary fate and consequences of duplicate genes. Science. 290 (5494), 1151–1155 (2020).Article 
ADS 

Google Scholar 
Smith, E. G. et al. Host specificity of Symbiodinium variants revealed by an ITS2 metahaplotype approach. ISME J. 11 (6), 1500–1503 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
Ding, X. X. et al. Developing population identification tool based on polymorphism of rDNA for traditional Chinese medicine: Artemisia annua L. Phytomedicine. 116, 154882 (2023).Article 
PubMed 

Google Scholar 
Obert, T. et al. Delimitation of five astome ciliate species isolated from the digestive tube of three ecologically different groups of lumbricid earthworms, using the internal transcribed spacer region and the hypervariable D1/D2 region of the 28S rRNA gene. BMC Evol. Biol. 20 (1), 37 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Liu, Z. W. et al. Molecular authentication of the medicinal species of Ligusticum (Ligustici Rhizoma et Radix, Gao-ben) by integrating non-coding internal transcribed spacer 2 (ITS2) and its secondary structure. Front. Plant. Sci. 9 (10), 429 (2019).Article 

Google Scholar 
Devi, M. P. et al. DNA barcoding and ITS2 secondary structure predictions in Taro (Colocasia esculenta L. Schott) from the north eastern hill region of India. Genes (Basel). 13 (12), 2294 (2022).Article 
PubMed 

Google Scholar 
Johzuka-Hisatomi, Y. et al. Efficient transfer of base changes from a vector to the rice genome by homologous recombination: involvement of heteroduplex formation and mismatch correction. Nucleic Acids Res. 36 (14), 4727–4735 (2008).Article 
PubMed 
PubMed Central 

Google Scholar 
Lesecque, Y. et al. GC-biased gene conversion in yeast is specifically associated with crossovers: molecular mechanisms and evolutionary significance. Mol. Biol. Evol. 30 (6), 1409–1419 (2013).Article 
PubMed 
PubMed Central 

Google Scholar 
Rousselle, M. et al. Influence of recombination and GC-biased gene conversion on the adaptive and nonadaptive substitution rate in mammals versus birds. Mol. Biol. Evol. 36 (3), 458–471 (2018).Article 
PubMed Central 

Google Scholar 
Rocha, E. P. et al. Base composition bias might result from competition for metabolic resources. Trends Genet. 18 (6), 291–294 (2002).Article 
PubMed 

Google Scholar 
Higgs, P. G. RNA secondary structure: physical and computational aspects. Q. Rev. Biophys. 33 (3), 199–253 (2000).Article 
PubMed 

Google Scholar 
Kiktev, D. A. et al. GC content elevates mutation and recombination rates in the yeast Saccharomyces cerevisiae. PNAS. 115 (30), E7109–7118 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Long, X. et al. Independent evolution of sex chromosomes and male pregnancy-related genes in two seahorse species. Mol. Biol. Evol. 40 (1), 279 (2023).Article 

Google Scholar 
Liu, A. et al. GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes. Genome Res. 33 (10), 1673–1689 (2023).Article 
PubMed 
PubMed Central 

Google Scholar 
Boman, J. et al. The effects of GC-biased gene conversion on patterns of genetic diversity among and across butterfly genomes. Genome Biol. Evol. 13 (5), 064 (2021).Article 

Google Scholar 

Hot Topics

Related Articles